Dr. Ana Stelline was in a bubble to safeguard her while the Replicant underground established an army. While this explanation is a bit lengthy, I believe it does tie together all the salient points.
I fail to understand how the side that has her in a bubble, making
memories, is moving forward with their (the replicants') plan?
We know that Deckard and the underground replicants wanted to protect Stelline knowing that even in hiding, they would still be hunted relentlessly. Deckard's part was that he was able to "scramble the records", fabricating evidence that twins were born, a boy and a girl.
When K is examining the DNA, he identifies a genetic anomaly that results in a compromised immune system--a story separately verified by Stelline, saying she was unable leave the planet and could only safely live in the bubble. The other way to look at this, however, is the genetic anomaly was a deliberate ruse to prevent her emigration off-world. That is, ensuring that no matter what happened to her in the orphanage or beyond, she would be marooned on earth.
Dr. Stelline: A compromised immune system. A life of freedom, so long as it’s behind glass.
K: Is that why you’re not off-world?
Dr. Stelline: Yes. My parents had our passes in-pocket, but I took sick.
Considering the squalor she endured in the scrapyard orphanage in San Diego, it is highly unlikely this immuno-compromised condition is real. This containment also had a happy by-product of keeping her insulated from physical danger.
She's now 30 years of age and they are no closer to finding out how
to have children of their own. Are they just having sex with each
other for 30 years hoping to hit the jackpot again?
The events of Blade Runner: Black Out 2022 chronicle how Replicants came to be prohibited after their assault on the world with an EMP. It is another ten years before the Wallace Corp is permitted to start up new production on Replicants. That means for Stelline's first 10 years of living, the zeitgeist of the world was heavily anti-replicant; not an environment that would be accepting of the notion that replicants are more human than they were given credit for.
So around 2032 marks the beginning of new Replicants (Nexus 8s under Wallace Corp), in which the underground Replicants are still unlikely to provide a real, physical (and existential) threat. There's a single manufacturer again and the replicants are ridiculously obedient. But as we've seen from the original BR as well as BR2049, believable memories seem to be the root causes of all the chaos. This would explain why (for the viewers' benefit) Stelline tells K that implanting real memories into replicants is illegal.
- Rachel--and her memories of Tyrell's niece (believed to be her own)--drives her to confront Deckard in his home and then run away.
- K (or Joe) believing to be the boy with the horse lies to Joshi about retiring the Replicant child.
I mean they lead us to believe she's more important than that, yet, they're not using her in any way to figure it out.
So ultimately, the underground resistance was just biding their time waiting for the best opportunity to show the world that they are as (or more) human than humans, and that they would be prepared and ready to fight/defend Stelline as their figurehead when they out her as a Replicant offspring.
Freysa: If a baby can come from one of us, we are our own masters. "More human
than humans". A revolution is coming. And we’re building an army. I
want to free our people. If you want to be free, join us. Deckard,
Sapper, you, me; our lives mean nothing next to a storm that’s coming. [...]
When the time comes, I will show her to the world. And she will lead our army.
In the meantime, all time "lost" in the interim just had the bonus of more Replicants being indoctrinated with Stelline's foreign-but-authentic memories. Presumably, this would be beneficial to the resistance in that they might be more sympathetic to the resistance's cause, as we saw in K. The technology for replicants to reproduce is limited to just Rachel, so they weren't hoping to just 'hit the jackpot'.
A question that doesn't seem to have good answer, however, is how the first Replicant offspring (some random kid from an orphanage) attained the skills and foot-in-the-door to become the world's foremost memory creator for Wallace Corp.